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Signal transduction is the fundamental mechanism for regulation of cellular activities by environmental cues and regulatory signals, and is particularly important for plants, whose survival requires proper physiological and developmental responses to the environmental changes. Much progress has been made recently in the plant signal transduction research field thanks to the development of diverse techniques which are covered in Plant Signalling Networks: Methods and Protocols. These include advanced research methods such as proteomics and mass spectrometry methods for studying protein modification, biochemical and cell biological tools for studying protein-protein interactions, genomic techniques for dissecting protein-DNA interaction and transcription networks, and computation methods that integrate molecular network into plant developmental processes.
Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Plant Signalling Networks: Methods and Protocols presents well-honed methodologies for a wide range of research approaches including genetics, proteomics, biochemical, cell biological, and computational approaches, and seeks to serve both professionals and novices with a comprehensive understanding of complex signaling networks in plants.
1. Experimental Analysis of Receptor Kinase Phosphorylation Srijeet K. Mitra, Michael B. Goshe, and Steven D. Clouse
2. Quantitative Measurement of Phosphopeptides and Proteins via Stable Isotope Labeling in Arabidopsis (SILIA) and Functional Phosphoproteomic Strategies Ning Li
3. Identification of O-GlcNAc Modified Proteins from Arabidopsis Shou-Ling Xu, Robert J. Chalkley, Zhi-Yong Wang, and Alma L. Burlingame
4. Quantitative Analysis of Protein Phosphorylation Using Two-Dimensional Difference Gel Electrophoresis (2-D DIGE) Zhiping Deng, Shuolei Bu, and Zhi-Yong Wang
5. Quantitative Analysis of Plasma Proteome Using Two-Dimensional Difference Gel Electrophoresis (2-D DIGE) Wenqiang Tang
6. Identification and Verification of Redox-Sensitive Proteins in Arabidopsis thaliana Hai Wang, Shengbing Wang, and Yiji Xia
7. Small-Molecule Dissection of Brassinosteroid (BR) Signaling Mirela-Corina Codreanu, Dominique Audenaert, Long Nguyen, Tom Beeckman, and Eugenia Russinova
8. A Chemical Genetics Method to Uncover Small Molecules for Dissecting the Mechanism of ABA Responses in Arabidopsis Seed Germination Yang Zhao
9. Activation Tagging Xiaoping Gou and Jia Li
10. Rho GTPase Activity Analysis in Plant Cells Tongda Xu
11. Analysis of In Vivo ROP GTPase Activity at the Subcellular Level by Fluorescence Resonance Energy Transfer Microscopy Lei Zhu and Ying Fu
12. In vivo Ubiquitination Assay by Agroinfiltration Lijing Liu, Qingzhen Zhao, and Qi Xie
13. In Vitro Protein Ubiquitination Assay Qingzhen Zhao, Lijing Liu, and Qi Xie
14. Genome-Wide Identification of Transcription Factor Binding Sites in Plants Using Chromatin Immunoprecipitation Followed by Microarray (ChIP-chip) or Sequencing (ChIP-seq) Jia-Ying Zhu, Yu Sun, and Zhi-Yong Wang
15. Smart Pooling of mRNA Samples for Efficient Transcript Profiling Raghunandan M. Kainkaryam, Angela Bruex, Peter J. Woolf, and John Schiefelbein
16. Transient Expression Assays for Quantifying Signaling Output Yajie Niu and Jen Sheen
17. Genome-Wide Profiling of Uncapped mRNA Yuling Jiao and Jose Luis Riechmann
18. Computational Tools for Quantitative Analysis of Cell Growth Patterns and Morphogenesis in Actively Developing Plant Stem Cell Niches Anirban Chakraborty, Ram Kishor Yadav, Min Liu, Moses Tataw, Katya Mkrtchyan, Amit Roy Chowdhury, and G. Venugopala Reddy
